Provide Mothur-compatible output files about swarm HOT 4 CLOSED

The output format of Mothur's clusters is described on that page: http://www.mothur.org/wiki/List_file

from swarm.

Appears to be fairly trivial to convert swarm's output to a mothur compatible list file:

tr '\n' '\t' < test.swarms > test.swarms.list.tmp1
tr ' ' ',' < test.swarms.list.tmp1 > test.swarms.list.tmp2
echo -e "d1\t12345\t" | cat test.swarms.list.tmp2 > test.list

where d1 is my -d level, and 12345 is the number of produced OTUs. Tested with mothurs make.shared command, then ran a short analysis on the shared file.

from swarm.

Hi Adam,

indeed it is trivial. If I may, I suggest some modifications to avoid using intermediate files:

SWARMS="test.swarms"
OTUs=$(wc -l < "${SWARMS}")
(echo -ne "d1\t${OTUs}\t" ; tr "\n" "\t" < "${SWARMS}" | tr " " ",") > test.list

I also used the -n option of echo to avoid the automatic \n character. What do you think of that code block?

from swarm.

This feature is now implemented in the SWARM code. Option -r or --mothur will format the output file according to the mothur list file format.

from swarm.